Treating cancer using an oligonucleotide N3′-&gt;N5′ thiophosphoramidate

ABSTRACT

Oligonucleotides with a novel sugar-phosphate backbone containing at least one internucleoside 3′-NHP(O)(S − )O-5′ linkage, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive thiophosphoramidate oligonucleotides were found to retain the high RNA binding affinity of the parent oligonucleotide N3′→P5′ phosphoramidates and to exhibit a much higher acid stability.

CROSS-REFERENCE TO RELATED APPLICATIONS

The application is a continuation of U.S. application Ser. No.10/463,076, filed Jun. 17, 2003 (now U.S. Pat. No. 6,835,826), which wasa continuation of U.S. application Ser. No. 09/657,445, filed Sep. 8,2000, (now U.S. Pat. No. 6,608,036), which claimed priority from U.S.Application No. 60/153,201, filed Sep. 10, 1999, and from U.S.Application No. 60/160,444, filed Oct 19, 1999, which are hereinincorporated by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to oligonucleotides having a novelsugar-phosphate backbone containing internucleoside 3′-NHP(O)(S⁻)O-5′linkages. More particularly, the present invention is directed tothiophosphoramidate oligonucleotide compositions, their use asdiagnostic or therapeutic agents and methods for synthesizingthiophosphoramidate oligonucleotides.

BACKGROUND OF THE INVENTION

Nucleic acid polymer chemistry has played a crucial role in manydeveloping technologies in the pharmaceutical, diagnostic, andanalytical fields, and more particularly in the subfields of antisenseand anti-gene therapeutics, combinatorial chemistry, branched DNA signalamplification, and array-based DNA diagnostics and analysis (e.g.Uhlmann and Peyman, Chemical Reviews, 90:543–584, 1990; Milligan et al.,J. Med. Chem., 36:1923–1937, 1993; DeMesmaeker et al., Current Opinionin Structural Biology, 5:343–355, 1995; Roush, Science, 276:1192–1193,1997; Thuong et al., Angew. Chem. Int. Ed. Engl., 32:666–690, 1993;Brenner et al., Proc. Natl. Acad. Sci., 89:5381–5383, 1992; Gold et al.,Ann. Rev. Biochem., 64:763–797, 1995; Gallop et al., J. Med. Chem.,37:1233–1258, 1994; Gordon et al., J. Med. Chem., 37:1385–1401, 1994;Gryaznov, International application PCT/US94/07557; Urdea et al., U.S.Pat. No. 5,124,246; Southern et al., Genomics, 13: 1008–1017, 1992;McGall et al., U.S. Pat. No. 5,412,087; Fodor et al., U.S. Pat. No.5,424,186; Pirrung et al., U.S. Pat. No. 5,405,783).

Much of this chemistry has been directed to improving the bindingstrength, specificity, and nuclease resistance of natural nucleic acidpolymers, such as DNA. Unfortunately, improvements in one property, suchas nuclease resistance, often involve trade-offs against otherproperties, such as binding strength. Examples of such trade-offsabound: peptide nucleic acids (PNAs) display good nuclease resistanceand binding strength, but have reduced cellular uptake in test cultures(e.g. Hanvey et al., Science, 258:1481–1485, 1992); phosphorothioatesdisplay good nuclease resistance and solubility, but are typicallysynthesized as P-chiral mixtures and display severalsequence-non-specific biological effects (e.g. Stein et al., Science,261:1004–1012, 1993); methylphosphonates display good nucleaseresistance and cellular uptake, but are also typically synthesized asP-chiral mixtures and have reduced duplex stability (e.g. Mesmaeker etal. (cited above); and so on.

Recently, a new class of oligonucleotide analog has been developedhaving so-called N3′→P5′ phosphoramidate internucleoside linkages whichdisplay favorable binding properties, nuclease resistance, andsolubility (Gryaznov and Letsinger, Nucleic Acids Research,20:3403–3409, 1992; Chen et al., Nucleic Acids Research, 23:2661–2668,1995; Gryaznov et al., Proc. Natl. Acad. Sci., 92:5798–5802, 1995; andGryaznov et al., J. Am. Chem. Soc., 116:3143–3144, 1994).Phosphoramidate compounds contain a 3′-amino group at each of the2′-deoxyfuranose nucleoside residues replacing a 3′-oxygen atom. Thesynthesis and properties of oligonucleotide N3′→P5′ phosphoramidates arealso described in Gryaznov et al., U.S. Pat. Nos. 5,591,607; 5,599,922;5,726,297; and Hirschbein et al., U.S. Pat. No. 5,824,793.

The oligonucleotide N3′→P5′ phosphoramidates form unusually stableduplexes with complementary DNA and especially RNA strands, as well asstable triplexes with DNA duplexes, and they are also resistant tonucleases (Chen et al., Nucleic Acids Research, 23:2661–2668, 1995;Gryaznov et al., Proc. Natl. Acad. Sci., 92:5798–5802, 1995). Moreoveroligonucleotide N3′→P5′ phosphoramidates are more potent antisenseagents than phosphorothioate derivatives both in vitro and in vivo(Skorski et al., Proc. Natl. Acad. Sci., 94:3966–3971, 1997). At thesame time the phosphoramidates apparently have a low affinity to theintra- and extracellular proteins and increased acid liability relativeto the natural phosphodiester counterparts (Gryaznov et al., NucleicAcids Research, 24:1508–1514, 1996). These features of theoligonucleotide phosphoramidates potentially adversely affect theirpharmacological properties for some applications. In particular, theacid stability of an oligonucleotide is an important quality given thedesire to use oligonucleotide agents as oral therapeutics.

In order to circumvent the above described problems associated witholigonucleotide analogs, a new class of compounds was sought thatembodies the best characteristics from both oligonucleotidephosphoramidates and phosphorothioates. The present invention describesthe synthesis, properties and uses of oligonucleotide N3′→P5′thiophosphoramidates.

SUMMARY OF THE INVENTION

The compositions and methods of the present invention relate topolynucleotides having contiguous nucleoside subunits joined byintersubunit linkages. In the polynucleotides of the present invention,at least two contiguous subunits are joined by a N3′→P5′thiophosphoramidate intersubunit linkage defined by the formula of3′-[—NH—P(═O)(—SR)—O—]-5′, wherein R is selected from the groupconsisting of hydrogen, alkyl, aryl and salts thereof. In a preferredembodiment of the invention, R is hydrogen or a salt thereof. Theinventive polynucleotides can be composed such that all of theintersubunit linkages are N3′→P5′ thiophosphoramidate. Alternatively,the polynucleotides of the invention can contain a second class ofintersubunit linkages such as phosphodiester, phosphotriester,methylphosphonate, P′3→N5′ phosphoramidate, N′3→P5′ phosphoramidate, andphosphorothioate linkages.

An exemplary N3′→P5′ thiophosphoramidate intersubunit linkage has theformula:

where B is a purine or pyrimidine or an analog thereof, Z is OR, SR, ormethyl, wherein R is selected from the group consisting of hydrogen,alkyl, and aryl and their salts; and R₁ is selected from the groupconsisting of hydrogen, O—R₂, S—R₂, and halogen, wherein R₂ is H, alkyl,or (CH₂)_(n)W(CH₂)_(m)H, where n is between 1–10, m is between 0–10 andW is O, S, or NH, with the proviso that when Z is methyl or OMe, R₁ isnot H. The nucleoside subunits making up the polynucleotides can beselected to be in a defined sequence: such as, a sequence of basescomplementary to a single-strand nucleic acid target sequence or asequence that will allow formation of a triplex structure between thepolynucleotide and a target duplex. The nucleoside subunits joined by atleast one N3′→P5′ thiophosphoramidate intersubunit linkage, as describedabove, have superior resistance to acid hydrolysis, yet retain the samethermal stability as compared to oligonucleotides having phosphoramidateintersubunit linkages.

The present invention also includes a method of synthesizing anoligonucleotide N3′→P5′ thiophosphoramidate. In this method a firstnucleoside 5′-succinyl-3′-aminotrityl-2′,3′-dideoxy nucleoside isattached to a solid phase support. The first nucleoside additionally hasa protected 3′ amino group. The protected 3′ amino group is thendeprotected to form a free 3′ amino group to which a second nucleosideis added. The free 3′ amino group of the first nucleoside is reactedwith a 3′-protectedaminonucleoside-5′-O-cyanoethyl-N,N-diisopropylaminophosphoramiditemonomer to form an internucleoside N3′→P5′ phosphoramidite linkage. Theinternucleaside phosphoramidite group is then sulfurized to form aN3′→P5′ thiophosphoramidate internucleaside linkage between the firstand second nucleosides.

In another embodiment of the invention, a method is provided forhybridizing a thiophosphoramidate oligonucleotide of the invention to aDNA or RNA target. The thiophosphoramidate polynucleotide comprises asequence of nucleoside subunits joined by at least one subunit definedby the formula:

where B is a purine or pyrimidine or an analog thereof, Z is OR, SR, ormethyl, and R₁ is selected from the group consisting of hydrogen, O—R₂,S—R₂, and halogen, wherein R₂ is H, alkyl, or (CH₂)_(n)W(CH₂)_(m)H,where n is between 1–10, m is between 0–10 and W is O, S, or NH, withthe proviso that when Z is methyl or OMe, R₁ is not H. Thethiophosphoramidate polynucleotide is contacted with the RNA target toallow formation of a hybridization complex between the polynucleotideand the RNA target.

The present invention also includes pharmaceutical compositions and kitsincluding a polynucleotide having at least one N3′→P5′thiophosphoramidate linkage, as described above. The inventiveoligonucleotides are particularly useful in oral therapeuticapplications based on hybridization, such as, antigene and antisenseapplications, including the inhibition of telomerase enzyme activity.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing aspects and many of the attendant advantages of thisinvention will become more readily appreciated as the same become betterunderstood by reference to the following detailed description, whentaken in conjunction with the accompanying drawings, wherein:

FIG. 1A shows the internucleoside linkage structure of oligonucleotidephosphorothioates;

FIG. 1B shows the internucleoside linkage structure of oligonucleotidephosphoramidates;

FIG. 1C shows the internucleoside linkage structure of exemplaryoligonucleotide thiophosphoramidates of the invention.

FIG. 2 shows a schematic outline of the step-by-step synthesis ofuniformly modified oligonucleotide thiophosphoramidates.

FIG. 3 shows a schematic outline of the conversion a dinucleotidethiophosphoramidate into its phosphoramidate counterpart, as well as theproducts resulting from the hydrolysis of the dinucleotidethiophosphoramidate.

FIG. 4 shows the results of an in vitro telomerase inhibition assayperformed using increasing amount of thiophosphoramidate oligonucleotideof SEQ ID NO:2 that is complementary to telomerase RNA, or SEQ ID NO:4that contains nucleotide mismatches.

FIG. 5 shows the results of an in vitro telomerase inhibition assayperformed using increasing amount of thiophosphoramidate oligonucleotideof SEQ ID NO:8 that is complementary to telomerase RNA.

FIG. 6 shows the results of SEQ ID NOs:2 and 8 that are complementary totelomerase RNA, and SEQ ID NO:4 that contains nucleotide mismatches onthe growth of HME50-5E cells.

FIG. 7 shows the results of the thiophosphoramidate oligonucleotides onthe telomere length of HME50-5E cells.

FIG. 8 illustrates the IC₅₀ values measured for the thiophosphoramidateoligonucleotide SEQ ID NO:2.

DETAILED DESCRIPTION

Definitions

An “alkyl group” refers to an alkyl or substituted alkyl group having 1to 20 carbon atoms, such as methyl, ethyl, propyl, and the like. Loweralkyl typically refers to C₁ to C₅. Intermediate alkyl typically refersto C₆ to C₁₀.

An “aryl group” refers to an aromatic ring group having 5–20 carbonatoms, such as phenyl, naphthyl, anthryl, or substituted aryl groups,such as, alkyl- or aryl-substitutions like tolyl, ethylphenyl,biphenylyl, etc. Also included are heterocyclic aromatic ring groupshaving one or more nitrogen, oxygen, or sulfur atoms in the ring.

“Oligonucleotides” typically refer to nucleoside subunit polymers havingbetween about 3 and about 50 contiguous subunits. The nucleosidesubunits can be joined by a variety of intersubunit linkages, including,but not limited to, those shown in FIGS. 1A to 1C. Further,“oligonucleotides” includes modifications, known to one skilled in theart, to the sugar backbone (e.g., ribose or deoxyribose subunits), thesugar (e.g., 2′ substitutions), the base, and the 3′ and 5′ termini. Theterm “polynucleotide”, as used herein, has the same meaning as“oligonucleotide” and is used interchangeably with “polynucleotide”.

Whenever an oligonucleotide is represented by a sequence of letters,such as “ATGUCCTG”, it will be understood that the nucleotides are in5′→3′ order from left to right.

As used herein, “nucleoside” includes the natural nucleosides, including2′-deoxy and 2′-hydroxyl forms, e.g. as described in Komberg and Baker,DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992), and analogs.“Analogs” in reference to nucleosides includes synthetic nucleosideshaving modified base moieties and/or modified sugar moieties, e.g.described generally by Scheit, Nucleotide Analogs (John Wiley, New York,1980). Such analogs include synthetic nucleosides designed to enhancebinding properties, e.g. stability, specificity, or the like, such asdisclosed by Uhlmann and Peyman (Chemical Reviews, 90:543–584, 1990).

A “base” is defined herein to include (i) typical DNA and RNA bases(uracil, thymine, adenine, guanine, and cytosine), and (ii) modifiedbases or base analogs (e.g., 5-methyl-cytosine, 5-bromouracil, orinosine). A base analog is a chemical whose molecular structure mimicsthat of a typical DNA or RNA base.

As used herein, “pyrimidine” means the pyrimidines occurring in naturalnucleosides, including cytosine, thymine, and uracil, and common analogsthereof, such as those containing oxy, methyl, propynyl, methoxy,hydroxyl, amino, thio, halo, and like, substituents. The term as usedherein further includes pyrimidines with common protection groupsattached, such as N₄-benzoylcytosine. Further common pyrimidineprotection groups are disclosed by Beaucage and Iyer (Tetrahedron48:223–2311, 1992).

As used herein, “purine” means the purines occurring in naturalnucleosides, including adenine, guanine, and hypoxanthine, and commonanalogs thereof, such as those containing oxy, methyl, propynyl,methoxy, hydroxyl, amino, thio, halo, and like, substituents. The termas used herein further includes purines with common protection groupsattached, such as N₂-benzoylguanine, N₂-isobutyrylguanine,N₆-benzoyladenine, and the like. Further common purine protection groupsare disclosed by Beaucage and Iyer (cited above).

As used herein, the term “-protected-” as a component of a chemical namerefers to art-recognized protection groups for a particular moiety of acompound, e.g. “5′-protected-hydroxyl” in reference to a nucleosideincludes triphenylmethyl (i.e., trityl), p-anisyldiphenylmethyl (i.e.,monomethoxytrityl or MMT), di-p-anisylphenylmethyl (i.e.,dimethoxytrityl or DMT), and the like. Art-recognized protection groupsinclude those described in the following references: Gait, editor,Oligonucleotide Synthesis: A Practical Approach (IRL Press, Oxford,1984); Amarnath and Broom, Chemical Reviews, 77:183–217, 1977; Pon etal., Biotechniques, 6:768–775, 1988; Ohtsuka et al., Nucleic AcidsResearch, 10:6553–6570, 1982; Eckstein, editor, Oligonucleotides andAnalogues: A Practical Approach (IRL Press, Oxford, 1991), Greene andWuts, Protective Groups in Organic Synthesis, Second Edition, (JohnWiley & Sons, New York, 1991), Narang, editor, Synthesis andApplications of DNA and RNA (Academic Press, New York, 1987), Beaucageand Iyer (cited above), and like references.

The term “halogen” or “halo” is used in its conventional sense to referto a chloro, bromo, fluoro or iodo substituent. In the compoundsdescribed and claimed herein, halogen substituents are generally fluoro,bromo, or chloro, preferably fluoro or chloro.

The compounds of the present invention may be used to inhibit or reducetelomerase enzyme activity and/or proliferation of cells havingtelomerase activity. In these contexts, inhibition or reduction of theenzyme activity or cell proliferation refer to a lower level of themeasured activity relative to a control experiment in which the enzymeor cells are not treated with the test compound. In particularembodiments, the inhibition or reduction in the measured activity is atleast a 10% reduction or inhibition. One of skill in the art willappreciate that reduction or inhibition of the measured activity of atleast 20%, 50%, 75%, 90% or 100% may be preferred for particularapplications.

The present invention is directed generally to oligonucleotidescontaining at least one thiophosphoramidate intersubunit linkage,methods of synthesizing such polynucleotides and methods of using theinventive oligonucleotides as therapeutic compounds and to indiagnostics.

The oligonucleotides are exemplified as having the formula:

wherein each B is independently selected to be a purine or pyrimidine oran analog thereof such as uracil, thymine, adenine, guanine, cytosine,5-methylcytosine, 5-bromouracil and inosine,

Z₁ is O or NH,

Z₂ is OR, SR, or methyl wherein R is selected from the group consistingof hydrogen, alkyl, aryl and salts thereof,

R₁ is selected from the group consisting of hydrogen, O—R₂, S—R₂, NHR₂and halogen, wherein R₂ is H, alkyl, or (CH₂)_(n)W(CH₂)_(m)H, where n isbetween 1–10, m is between 0–10 and W is O, S, or NH,

R₃ and R₄ are selected from the group consisting of hydroxyl, amino andhydrogen, and

m₂ is an integer between 1 and 50.

The nucleoside subunits making up the polynucleotides of the presentinvention can be selected to be in a defined sequence: such as, asequence of bases capable of hybridizing specifically to a single-strandnucleic acid target sequence or a sequence that will allow formation ofa triplex structure between the polynucleotide and a target duplex.Preferably, the sequence of nucleoside subunits are joined by at leastone subunit that is a N3′→P5′ thiophosphoramidate defined by theformula:

wherein B is a purine or pyrimidine or an analog thereof;

Z is OR, SR, or methyl, wherein R is selected from the group consistingof hydrogen, alkyl, aryl and salts thereof; and

R₁ is selected from the group consisting of hydrogen, O—R₂, S—R₂, andhalogen, wherein R₂ is H, alkyl, or (CH₂)_(n)W(CH₂)_(m)H, where n isbetween 1–10, m is between 0–10 and W is O, S, or NH, with the provisothat when Z is methyl or OMe, R₁ is not H.

For example, all of the inter-subunit linkages of the polynucleotide canbe N3′→P′5 thiophosphoramidate inter-subunit linkages defined by theformula:

The inventive oligonucleotides can be used to hybridize to targetnucleic acid sequences such as RNA and DNA. When desirable, theoligonucleotides of the present invention can be labeled with a reportergroup, such as radioactive labels, biotin labels, fluorescent labels andthe like, to facilitate the detection of the polynucleotide itself andits presence in, for example, hybridization complexes.

In another aspect of the invention, a kit for isolating or detecting atarget RNA from a sample is provided. The kit contains anoligonucleotide having a defined sequence of nucleoside subunits joinedby a least one intersubunit linkage defined by the formula:

where B is a purine or pyrimidine or an analog thereof; Z is OR, SR, ormethyl; and R₁ is selected from the group consisting of hydrogen, O—R₂,S—R₂, and halogen, wherein R₂ is H, alkyl, or (CH₂)_(n)W(CH₂)_(m)H,where n is between 1–10, m is between 0–10 and W is O, S, or NH, withthe proviso that when Z is methyl or OMe, R₁ is not H, and

wherein the oligonucleotide hybridizes to the target RNA.

The oligonucleotides can also be formulated as a pharmaceuticalinhibition of transcription or translation in a cell in a diseasecondition related to overexpression of the target gene.

Preferably, the sequence of nucleoside subunits are joined by at leastone inter-subunit linkage that is a N3′→P5′ thiophosphoramidate.Alternatively, all of the inter-subunit linkages of the polynucleotideare N3′→P′5 thiophosphoramidate inter-subunit linkages defined by theformula:

In other aspects, the invention is directed to a solid phase method ofsynthesizing oligonucleotide N3′→P5′ thiophosphoramidates using amodification of the phosphoramidite transfer methodology of Nelson etal. (J. Organic Chemistry 62:7278–7287, 1997). The synthetic strategyemployed 3′-NH-trityl-protected 3′-aminonucleoside5′-O-cyanoethyl-N,N-diisopropylaminophosphoramidites (Nelson et al.,cited above) that were purchased from Cruachem and JBL Scientific, Inc.(Aston, Pa. and San Luis Obispo, Calif., respectively). Every syntheticcycle (see FIG. 2) was conducted using the following chemicalprocedures: 1) detritylation, 2) coupling; 3) capping; 4) sulfurization.For a step-wise sulfurization of the internucleaside phosphoramiditegroup formed after the coupling step, the iodine/water based oxidizingagent was replaced by the sulfurizing agents—either by elemental sulfurS₈ or by the commonly used Beaucage reagent—3H-1,2-benzodithiol-3-one1,1 dioxide (Iyer et al., J. Organic Chemistry, 55:4693–4699, 1990). Theoligonucleotide syntheses were performed (1 μmole synthesis scale) witha 1% solution of Beaucage reagent in anhydrous acetonitrile or 15% S₈ inCS₂/Et₃N, 99/1 (vol/vol) as the sulfurizing agent.

Chimeric N3′→P5′ phosphoramidate-phosphorthioamidate oligonucleotidescan be made by using an oxidation step(s) after the coupling step, whichresults in formation of a phosphoramidate internucleoside group.Similarly, phosphodiester-phosphorthioamidates can be made by using5′-phosphoramidite-3′-O-DMTr-protected nucleotides as monomeric buildingblocks. These synthetic approaches are known in the art.

The model phosphoramidate thymidine dinucleoside TnpsTn was preparedusing both types of sulfurizing agents and has a 3′-NHP(O)(S⁻)O-5′internucleoside group. The reaction mixtures were analyzed and structureof the compound was confirmed by ion-exchange (IE) and reverse phase(RP) HPLC, and ³¹P NMR. The analysis revealed that sulfurization of theinternucleoside phosphoramidite group with Beaucage reagent resulted information of approximately 10–15% of the oxidized dinucleoside with3′-NHP(O)(O⁻)O-5′ phosphoramidate linkage (³¹P NMR δ, ppm 7.0 in D₂O).Alternatively, sulfurization with molecular sulfur S₈ produced thedesired dinucleotide containing 3′-NHP(O)(S⁻)O-5′ internucleoside groupwith practically quantitative yield, as was judged by ³¹P NMR and IEHPLC analysis (³¹P NMR δ, ppm 56.4, 59.6 in D₂O, Rp,Sp isomers).

Similar results with regards to the sulfurization efficiency wereobtained for the synthesis of model oligonucleotide 11-mer GTTAGGGTTAG(SEQ ID NO:1), where sulfurization with Beaucage reagent resulted in thefull length product containing ˜15% phosphoramidate linkages, as wasjudged by ³¹P NMR analysis of the reaction mixture. Chemical shifts forthe main peaks were ˜57 and 60 ppm (broad doublets) and 7 ppm (broadsinglet) corresponding to the thiophosphoramidate and phosphoramidategroups, respectively. In contrast, sulfurization with S₈ produced only˜2% phosphoramidate linkages in the 11-mer product according to the ³¹PNMR analysis. The IE HPLC analysis of the oligomer was in good agreementwith the ³¹P NMR spectrum. Structure and purity of the finaloligonucleotide products was confirmed by MALDI-TOF mass spectraanalysis, by ³¹P NMR, and by polyacrylamide gel electrophoreticanalysis. The molecular mass for thiophosphoramidate oligomersGT₂AG₃T₂AG (SEQ ID NO:1) and TAG₃T₂AGACA₂ (SEQ ID NO:2) was calculatedto be 3,577.11 and 4,202.69, respectively. The molecular mass forthiophosphoramidate oligomers GT₂AG₃T₂AG (SEQ ID NO:1) and TAG₃T₂AGACA₂(SEQ ID NO:2) was determined experimentally by MALDI-TOF massspectroscopy to be 3,577 and 4,203 respectively; mobility in 15% PAGErelative to isosequential phosphoramidates was 0.95 and 0.97respectively.

The model phosphoramidate nucleoside TnpsTn was quantitatively convertedinto the phosphoramidate counterpart TnpTn, by treatment with 0.1 Miodine solution in pyridine/THF/H₂O 1/4/0.1 (vol/vol), 55° C., 15 min,as judged by IE HPLC and ³¹P NMR ³¹P NMR δ ppm 7.0) (see FIG. 3).Treatment of the TnpsTn dinucleotide with 10% acetic acid, 55° C., 48 hrunexpectedly resulted in only partial hydrolysis (˜10%) ofinternucleoside phosphoramidate linkage. For comparison under theseconditions the parent phosphoramidate dimer TnpTn was completelyhydrolyzed. Cleavage of the N—P bond in the dinucleotidethiophosphoramidate was accompanied by concomitant de-sulfurizationprocess (˜15%), followed by a rapid hydrolysis of the resultantphosphoramidate —NHP(O)(O⁻)O— group as revealed by IE HPLC and ³¹P NMR(FIG. 3).

The 2′-R₃ N3′→P5′ thiophosphoramidates can be obtained from thecorresponding phosphoramidates as described above. The 2′-R₃ N3′→P5′phosphoramidates were obtained by the phosphoramidite transfermethodology devised for the synthesis of oligonucleotide N3′→P5′phosphoramidates. The synthesis of 2-O-alkyl N3′→P5′thiophosphoramidates is described in detail as an illustration of thismethodology.

The appropriately protected2′-O-alkyl-3′aminonucleoside-5′-phosphoramidite building blocks 4, 6,11, and 15, where alkyl is methyl, were prepared according to a seriesof chemical transformations shown in Schemes 1–3 below. An inventivestep for the preparation of these compounds was the selectivemethylation of the 2′-hybroxyl group in the presence of either the iminofunctionality of pyrimidines, or the N-7 atom of the purines. The twopyrimidine-based monomers were obtained from the known3-azido-2′-O-acetyl-5′-O-toluoyl-3′-deoxy-β-D-ribofuranosyluracil 1.Typically, the N-3/O-4 imino nitrogen of 1 was first protected with aprotecting group, such as by the reaction of methyl propyolate in thepresence of dimethylaminopyridine (Scheme 1). The crude reaction productwas then selectively 2′-O-deaectylated,

and the resulting free 2′-hydroxyl group was then alkylated, such as bymethylation using iodomethane and silver oxide. The N-3 protecting groupwas removed and the 3′-azido group was reduced to amine, which was thenimmediately protected, such as reaction with4-monomethoxytritylchloride, to give the precursor 3. The 5′-toluoylester was then cleaved using an alkaline solution, followed byphosphitylation using known protocols to give the desired 2′-O-methyluridine phosphoramidite monomer 4. The 2′-O-methyl cytosinephosphoramidite was obtained by conversion of uridine intermediate 3into 3′-aminocytidine analogue 5.

The synthesis of the 2′-O-alkyl adenosine analogue required the use ofbulky protecting groups, primarily for exocyclic amine in order toprevent the alkylation of N-7 during methylation of the 2′-hydroxylgroup (Scheme 2).3′-Azido-2′-O-acetyl-5′-O-toluoyl-N⁶-benzoyl-3′-deoxyadenosine 7 wasfirst deprotected, such as by reaction with NH₃/MeOH (1/1, v/v), toafford 3′-azido-3′-deoxyadenosine. Then, the 5′-hydroxyl group and theN-6 moiety 15 were selectively re-protected with bulky protectinggroups, such as the t-butyldiphenylsilyl group or the4-monomethoxytrityl group. The combination of the two large substituentsat the 5′-O and N-6 positions sterically occluded N-7, thereby allowingfor the selective introduction of a methyl group at the 2′-position toproduce the intermediate 8. The N-6 4-monomethoxytrityl group was thenremoved, such as by treatment with 3% trichloroacetic acid in an organicsolvent, such as dichloromethane, followed by re-protection of N-6. Theuse of benzoyl chloride for the re-protection of N-6 resulted in theaddition of two benzoyl groups. The second benzoyl group wassubsequently removed by base treatment to produce the intermediate 9.The azide group was then reduced and the resulting 3′-amino group wasprotected with 4-monomethoxytrityl to form 10. Finally, the 5′-silylprotecting group was cleaved, and phosphitylation resulted in the2′-O-methyl phosphoramidite monomer 11.

The synthesis of the guanosine-based 2′-O-alkyl phosphoramidite 15 isdepicted in Scheme 3.3′-Azido-2′-O-acetyl-5′-O-toluoyl-N²-isobutryl-O⁶-diphenylcarbamoyl-3′-deoxyguanosine12 was deblocked by treatment with a base. The 5′O— and O-6 werereprotected by reaction with t-butyldiphenylsilylchloride. Thebis-silylated intermediate was then 2′-O alkylated. The O-6 silyl groupwas selectively deprotected to give compound 13. The N-2 group wasre-protected, the 3′-azido group was reduced, and the resulting 3′-aminogroup was protected to yield the nucleoside 14. Finally, the 2′-O-alkylguanosine phosphoramidite monomer 15 was obtained by removing the5′-protecting group followed by phosphitylation of the unmasked5′-hydroxyl.

In another embodiment of the present invention, the acid stability ofoligonucleotides is increased by placing subunits linked by N3′→P5′thiophosphoramidate intersubunit linkages in the oligonucleotides. Thehybridization properties of the thiophosphoramidate oligonucleotideswere evaluated relative to complementary DNA or RNA strands havingphosphodiester or phosphoramidate intersubunit linkages. The thermalstability data for duplexes generated from phosphoramidateoligonucleotides and phosphodiester oligomers are summarized in TABLE 1(Example 3).

Hybridization of the thiophosphoramidate oligonucleotides withcomplementary nucleic acids is sequence specific and determined by theproper Watson-Crick base pairing. The duplex formed by phosphoramidateoligonucleotide SEQ ID NO:3 with a single base mismatch with a RNAtarget component of telomerase (Example 6, TABLE 2, Experiment 2) issubstantially less stable than the duplex formed with oligonucleotideSEQ ID NO:1 which is fully complementary to the RNA component oftelomerase (Example 6, TABLE 2, Experiment 1).

Applications of Oligonucleotides Containing Internucleoside3′-NHP(O)(S⁻)O-5′ Thiophosphoramidate Linkages

Oligonucleotide SEQ ID NO:2 3′-NHP(O)(S⁻)O-5′ thiophosphoramidate wassynthesized. This compound was surprisingly acid stable and formed astable complex with a complementary RNA target. The N3′→P5′thiophosphoramidate polynucleotides of the present invention have greatpotential for anti-sense and anti-gene diagnostic/therapeuticapplications. In a preferred embodiment of the present invention, theoligonucleotides are oligodeoxyribonucleotides.

A. Telomerase Inhibition Applications

Recently, an understanding of the mechanisms by which normal cells reachthe state of senescence, i.e., the loss of proliferative capacity thatcells normally undergo in the cellular aging process, has begun toemerge. The DNA at the ends, or telomeres, of the chromosomes ofeukaryotes usually consists of tandemly repeated simple sequences.Scientists have long known that telomeres have an important biologicalrole in maintaining chromosome structure and function. More recently,scientists have speculated that the cumulative loss of telomeric DNAover repeated cell divisions may act as a trigger of cellular senescenceand aging, and that the regulation of telomerase, an enzyme involved inthe maintenance of telomere length, may have important biologicalimplications. See Harley, 1991, Mutation Research, 256:271–282.Experiments by Bodnar et al. have confirmed the importance of telomeresand telomerase in controlling the replicative lifespan of culturednormal human cells. See Bodnar et al., 1998, Science 279:349–352.

Telomerase is a ribonucleoprotein enzyme that synthesizes one strand ofthe telomeric DNA using as a template a sequence contained within theRNA component of the enzyme. See Blackburn, 1992, Annu. Rev. Biochem.,61:113–129. The RNA component of human telomerase has been sequenced andis 460 nucleotides in length containing a series of 11-base sequencerepeats that is complementary to the telomere repeat. Human telomeraseactivity has been inhibited by a variety of oligonucleotidescomplementary to the RNA component of telomerase. See Norton et al.,Nature Biotechnology, 14:615, 1996; Pitts et al., Proc. Natl. Acad.Sci., 95:11549–11554, 1998; and Glukhov et al., Bioch. Biophys. Res.Commun., 248:368–371, 1999. Thiophosphoramidate oligonucleotides of thepresent invention are complementary to 10 to 50 nucleotides oftelomerase RNA. Preferably, the inventive telomerase inhibitorthiophosphoramidate oligonucleotides have a 10 to 20 consecutive basesequence that is complementary to telomerase RNA.

Methods for detecting telomerase activity, as well as for identifyingcompounds that regulate or affect telomerase activity, together withmethods for therapy and diagnosis of cellular senescence andimmortalization by controlling telomere length and telomerase activity,have also been described. See Feng et al., 1995, Science, 269:1236–1241;Kim et al., 1994, Science, 266:2011–2014; PCT patent publication No.93/23572, published Nov. 25, 1993; and U.S. Pat. Nos. 5,656,638;5,760,062; 5,767,278; 5,770,613 and 5,863,936.

The identification of compounds that inhibit telomerase activityprovides important benefits to efforts at treating human disease.Compounds that inhibit telomerase activity can be used to treattelomerase-mediated disorders, such as cancer, since cancer cellsexpress telomerase activity and normal human somatic cells do notpossess telomerase activity at biologically relevant levels (i.e., atlevels sufficient to maintain telomere length over many cell divisions).Unfortunately, few such compounds, especially compounds with highpotency or activity and compounds that are bioavailable after oraladministration, have been identified and characterized. Hence, thereremains a need for compounds that act as telomerase inhibitors that haverelatively high potency or activity and that are orally bioavailable,and for compositions and methods for treating cancer and other diseasesin which telomerase activity is present abnormally.

The new thiophosphoramidate oligonucleotide compounds of the presentinvention are acid stable, and therefore, have many valuable uses asinhibitors of deleterious telomerase activity, such as, for example, inthe treatment of cancer in humans. Pharmaceutical compositions ofthiophosphoramidate oligonucleotide can be employed in treatmentregimens in which cancer cells are inhibited, in vivo, or can be used toinhibit cancer cells ex vivo. Thus, this invention provides therapeuticcompounds and compositions for treating cancer, and methods for treatingcancer in mammals (e.g., cows, horses, sheep, steer, pigs and animals ofveterinary interest such as cats and dogs). In addition, thephosphoramidate oligonucleotides of the present invention may also beused to treat other telomerase-mediated conditions or diseases, such as,for example, other hyperproliferative or autoimmune disorders.

As noted above, the immortalization of cells involves inter alia theactivation of telomerase. More specifically, the connection betweentelomerase activity and the ability of many tumor cell lines to remainimmortal has been demonstrated by analysis of telomerase activity (Kimet al., see above). This analysis, supplemented by data that indicatesthat the shortening of telomere length can provide the signal forreplicative senescence in normal cells, see PCT Application No.93/23572, demonstrates that inhibition of telomerase activity can be aneffective anti-cancer therapy. Thus, telomerase activity can prevent theonset of otherwise normal replicative senescence by preventing thenormal reduction of telomere length and the concurrent cessation of cellreplication that occurs in normal somatic cells after many celldivisions. In cancer cells, where the malignant phenotype is due to lossof cell cycle or growth controls or other genetic damage, an absence oftelomerase activity permits the loss of telomeric DNA during celldivision, resulting in chromosomal rearrangements and aberrations thatlead ultimately to cell death. However, in cancer cells havingtelomerase activity, telomeric DNA is not lost during cell division,thereby allowing the cancer cells to become immortal, leading to aterminal prognosis for the patient. Agents capable of inhibitingtelomerase activity in tumor cells offer therapeutic benefits withrespect to a wide variety of cancers and other conditions (e.g., fungalinfections) in which immortalized cells having telomerase activity are afactor in disease progression or in which inhibition of telomeraseactivity is desired for treatment purposes. The telomerase inhibitors ofthe invention can also be used to inhibit telomerase activity in germline cells, which may be useful for contraceptive purposes.

In addition, it will be appreciated that therapeutic benefits fortreatment of cancer can be realized by combining a telomerase inhibitorof the invention with other anti-cancer agents, including otherinhibitors of telomerase such as described in U.S. Pat. Nos. 5,656,638;5,760,062; 5,767,278; 5,770,613 and 5,863,936. The choice of suchcombinations will depend on various factors including, but not limitedto, the type of disease, the age and general health of the patient, theaggressiveness of disease progression, the TRF length and telomeraseactivity of the diseased cells to be treated and the ability of thepatient to tolerate the agents that comprise the combination. Forexample, in cases where tumor progression has reached an advanced state,it may be advisable to combine a telomerase inhibiting compound of theinvention with other agents and therapeutic regimens that are effectiveat reducing tumor size (e.g. radiation, surgery, chemotherapy and/orhormonal treatments). In addition, in some cases it may be advisable tocombine a telomerase inhibiting agent of the invention with one or moreagents that treat the side effects of a disease, e.g., an analgesic, oragents effective to stimulate the patient's own immune response (e.g.,colony stimulating factor).

The compounds of the present invention demonstrate inhibitory activityagainst telomerase activity in vivo, as can be demonstrated as describedbelow. The in vitro activities of the compounds of the invention hasalso been demonstrated using the methods described herein. As usedherein, the term “in vitro” refers to tests performed using living cellsin tissue culture. Such procedures are also known as “ex vivo”.

Oligonucleotide telomerase inhibitors described in this sectiontypically comprise a sequence that is complementary to telomerase RNAcomponent. The sequence of human telomerase RNA component is provided inU.S. Pat. No. 5,776,679. The telomerase RNA component of other speciescan also be used, depending on the intended subject of the therapy.

Generally, the oligonucleotide will comprise between about 10 and 100nucleotides that are specific for telomerase (that is, they hybridizewith telomerase RNA component at lower concentrations or underconditions of greater stringency than they will with other RNA enzymecomponents, or other RNA molecules expected to be present andfunctionally active in the target cells or therapeutic bystander cells).Included are oligonucleotides between about 10 and 25 nucleotides,exemplified by oligonucleotides between 12 and 15 nucleotides,illustrated in the Examples below. In many circumstances, theoligonucleotide will be exactly complementary to a consecutive sequenceof the same length in telomerase RNA. Nevertheless, it is understoodthat hybridization can still be specific even when there are mismatchedresidues or gaps or additions in the oligonucleotide, especially whenthe length of the corresponding complementary sequence in the RNA islonger than 15 nucleotides.

One method used to identify thiophosphoramidate polynucleotides of theinvention with specific sequences that inhibit telomerase activityinvolves placing cells, tissues, or preferably a cellular extract orother preparation containing telomerase in contact with several knownconcentrations of a thiophosphoramidate oligonucleotide that iscomplementary to the RNA component of telomerase in a buffer compatiblewith telomerase activity. The level of telomerase activity for eachconcentration of the thiophosphoramidate polynucleotide is measured.Before and after administration of a telomerase inhibitor, telomeraseactivity can be determined using standard reagents and methods. Forexample, telomerase acvitity in cultured cells can be measured usingTRAP activity assay (Kim et al., Science 266:2011, 1997; Weinrich etal., Nature Genetics 17:498, 1997). The following assay kits areavailable commercially for research purposes: TRAPeze® XK TelomeraseDetection Kit (Cat. s7707, Intergen Co., Purchase NY); and TeloTAGGGTelomerase PCR ELISAplus (Cat. 2,013,89, Roche Diagnostics, IndianapolisInd.).

The IC₅₀ (the concentration of the polynucleotide at which the observedactivity for a sample preparation is observed to fall one-half of itsoriginal or a control value) for the polynucleotide is determined usingstandard techniques. Other methods for determining the inhibitoryconcentration of a compound of the invention against telomerase can beemployed as will be apparent to those of skill in the art based on thedisclosure herein.

With the above-described methods, IC₅₀ values for several of thethiophosphoramidate oligonucleotides of the present invention weredetermined, and found to be below 10 nM (see TABLE 2, Example 6).

With respect to the treatment of malignant diseases usingthiophosphoramidate polynucleotides that are complementary to the RNAcomponent of telomerase are expected to induce crisis intelomerase-positive cell lines. Treatment of HME50-5E human breastepithelial cells that were spontaneously immortalized withthiophosphoramidate oligonucleotide SEQ ID NO:2 resulted in inhibitionof telomerase activity as demonstrated by the decrease in telomerelength (see Example 6, and FIG. 4). Treatment of othertelomerase-positive cell lines, such as HEK-293 and HeLa cells, withinventive thiophosphoramidate oligonucleotides that are complementary tothe RNA sequence component of telomerase is also expected to induce areduction of telomere length in the treated cells.

Thiophosphoramidate oligonucleotides of the invention are also expectedto induce telomere reduction during cell division in human tumor celllines, such as the ovarian tumor cell lines OVCAR-5 and SK-OV-3.Importantly, however, in normal human cells used as a control, such asBJ cells of fibroblast origin, the observed reduction in telomere lengthis expected to be no different from cells treated with a controlsubstance, e.g., a thiophosphoramidate oligonucleotide that has at leastone single base mismatch with the complementary telomerase RNA target.The thiophosphoramidate oligonucleotides of the invention also areexpected to demonstrate no significant cytotoxic effects atconcentrations below about 20 μM in the normal cells.

In addition, the specificity of the thiophosphoramidate oligonucleotidesof the present invention for telomerase RNA can be determined byperforming hybridization tests with and comparing their activity (IC₅₀)with respect to telomerase and to other enzymes known to have essentialRNA components, such as ribonucleoase P. Compounds having lower IC₅₀values for telomerase as compared to the IC₅₀ values toward the otherenzymes being screened are said to possess specificity for telomerase.

In vivo testing can also be performed using a mouse xenograft model, forexample, in which OVCAR-5 tumor cells are grafted onto nude mice, inwhich mice treated with a thiophosphoramidate oligonucleotide of theinvention are expected to have tumor masses that, on average, mayincrease for a period following the initial dosing, but will begin toshrink in mass with continuing treatment. In contrast, mice treated witha control (e.g., a thiophosphoramidate oligonucleotide that has at leastone single base mismatch with the complementary telomerase RNA target)are expected to have tumor masses that continue to increase.

From the foregoing those skilled in the art will appreciate that thepresent invention also provides methods for selecting treatment regimensinvolving administration of a thiophosphoramidate oligonucleotide of theinvention. For such purposes, it may be helpful to perform a terminalrestriction fragment (TRF) analysis in which DNA from tumor cells isanalyzed by digestion with restriction enzymes specific for sequencesother than the telomeric (T₂AG₃)_(N) sequence. Following digestion ofthe DNA, gel electrophoresis is performed to separate the restrictionfragments according to size. The separated fragments are then probedwith nucleic acid probes specific for telomeric sequences to determinethe lengths of the terminal fragments containing the telomere DNA of thecells in the sample. By measuring the length of telomeric DNA, one canestimate how long a telomerase inhibitor should be administered andwhether other methods of therapy (e.g., surgery, chemotherapy and/orradiation) should also be employed. In addition, during treatment, onecan test cells to determine whether a decrease in telomere length overprogressive cell divisions is occurring to demonstrate treatmentefficacy.

Thus, in one aspect, the present invention provides compounds that canserve in the war against cancer as important weapons againstmalignancies expressing telomerase, tumors including skin, connectivetissue, adipose, breast, lung, stomach, pancreas, ovary, cervix, uterus,kidney, bladder, colon, prostate, central nervous system (CNS), retinaand circulating tumors (such as leukemia and lymphoma). In particular,the thiophosphoramidate polynucleotides of the present invention canprovide a highly general method of treating many, if not most,malignancies, as demonstrated by the highly varied human tumor celllines and tumors having telomerase activity. More importantly, thethiophosphoramidate oligonucleotides of the present invention can beeffective in providing treatments that discriminate between malignantand normal cells to a high degree, avoiding many of the deleteriousside-effects present with most current chemotherapeutic regimes whichrely on agents that kill dividing cells indiscriminately.

B. Other Antisense Applications

Antisense therapy involves the administration of exogenousoligonucleotides that bind to a target nucleic acid, typically an RNAmolecule, located within cells. The term antisense is so given becausethe oligonucleotides are typically complementary to mRNA molecules(“sense strands”) which encode a cellular product.

The thiophosphoramidate oligonucleotides described herein are useful forantisense inhibition of gene expression (Matsukura et al., Proc. Natl.Acad. Sci., 86:4244–4248, 1989; Agrawal et al., Proc. Natl. Acad. Sci.,86:7790–7794, 1989; Zamecnik et al., Proc. Natl. Acad. Sci.,83:4143–4146, 1986; Rittner and Sczakiel, Nucleic Acids Research,19:1421–1426, 1991; Stein and Cheng, Science, 261:1004–1012, 1993).Oligonucleotides containing N3′→P5′ thiophosphoramidate linkages havetherapeutic applications for a large number of medically significanttargets, including, but not limited to inhibition of cancer cellproliferation and interference with infectious viruses. The N3′→P5′thiophosphoramidate oligonucleotides are useful for both veterinary andhuman applications. The high acid stability of the inventiveoligonucleotides and their ability to act effectively as antisensemolecules at low concentrations (see below) make these oligonucleotideshighly desirable as therapeutic antisense agents.

Anti-sense agents typically need to continuously bind all target RNAmolecules so as to inactivate them or alternatively provide a substratefor endogenous ribonuclease H (Rnase H) activity. Sensitivity ofRNA/oligonucleotide complexes, generated by the methods of the presentinvention, to Rnase H digestion can be evaluated by standard methods(Donia et al., J. Biol. Chem., 268:14514–14522, 1993; Kawasaki et al.,J. Medicinal Chem., 36:831–841, 1993).

The compounds and methods of the present invention provide severaladvantages over the more conventional antisense agents. First,thiophosphoramidate oligonucleotides bind more strongly to RNA targetsas corresponding phosphodiester oligonucleotides. Second, thethiophosphoramidate oligonucleotides are more resistant to degradationby acid conditions. Third, in cellular uptake of the compound, anuncharged thiophosphoramidate polynucleotide backbone may allow moreefficient entry of the phosphoramidate oligonucleotides into cells thana charged oligonucleotide.

Further, when an RNA is coded by a mostly purine strand of a duplextarget sequence, phosphoramidate analog oligonucleotides targeted to theduplex also have potential for inactivating the DNA—i.e., the ability toinactivate a pathogen in both single-stranded and double-stranded forms(see discussion of anti-gene therapies below).

Sequence-specific thiophosphoramidate oligonucleotide molecules arepotentially powerful therapeutics for essentially any disease orcondition that in some way involves RNA. Exemplary modes by which suchsequences can be targeted for therapeutic applications include:

a) targeting RNA sequences expressing products involved in thepropagation and/or maintenance infectious agents, such as, bacteria,viruses, yeast and other fungi, for example, a specific mRNA encoded byan infectious agent;

b) formation of a duplex molecule that results in inducing the cleavageof the RNA (e.g., Rnase H cleavage of RNA/DNA hybrid duplex molecules);

c) blocking the interaction of a protein with an RNA sequence (e.g., theinteraction of TAT and TAR, see below); and

d) targeting sequences causing inappropriate expression or proliferationof cellular genes: for example, genes associated with cell cycleregulation; inflammatory processes; smooth muscle cell (SMC)proliferation, migration and matrix formation (Liu et al., Circulation,79:1374–1387, 1989); certain genetic disorders; and cancers(protooncogenes).

In one embodiment, translation or RNA processing of inappropriatelyexpressed cellular genes is blocked. Exemplary potential targetsequences are protooncogenes, for example, including but not limited tothe following: c-myc, c-myb, c-fos, c-kit, ras, and BCR/ABL (e.g.,Wickstrom, Editor, Prospects for Antisense Nucleic Acid Therapy ofCancer and AIDS, Wiley-Liss, New York, N.Y., 1991; Zalewski et al.,Circulation Res., 88:1190–1195, 1993; Calabretta et al., Seminars inCancer Biol., 3:391–398, 1992; Calabretta et al., Cancer Treatment Rev.19:169–179, 1993), oncogenes (e.g., p 53, Bayever et al. AntisenseResearch and Development, 3:383–390, 1993), transcription factors (e.g.,NF.kappa.B, Cogswell et al., J. Immunol., 150:2794–2804, 1993) and viralgenes (e.g., papillomaviruses, Cowsert et al., Antimicrob. Agents andChemo., 37:171–177, 1993; herpes simplex virus, Kulka et al., AntiviralRes., 20:115–130, 1993). Another suitable target for antisense therapyin hyperplasias is the protein component of telomerase (see WO99/50279), which is often the limiting component in telomeraseexpression. The sequence of human telomerase reverse transcriptase isprovided in issued U.S. Pat. No. 6,093,809, in WO 98/14592, and inpGRN121 (ATCC Accession No. 209016). To further illustrate, two RNAregions of the HIV-1 protein that can be targeted by the methods of thepresent invention are the REV-protein response element (RRE) and theTAT-protein transactivation response element (TAR). REV activityrequires the presence of the REV response element (RRE), located in theHIV envelope gene (Malim et al., Nature, 338:254–257, 1989; Malim etal., Cell, 58:205–214, 1989).

The RRE has been mapped to a 234-nucleotide region thought to form fourstem-loop structures and one branched stem-loop structure (Malim et al.,Nature, 338:254–257, 1989). Data obtained from footprinting studies(Holland et al., J. Virol., 64:5966–5975, 1990; Kjems et al., Proc.Natl. Acad. Sci., 88:683–687, 1991) suggest that REV binds to six basepairs in one stem structure and to three nucleotides in an adjacentstem-loop structure of the RRE. A minimum REV binding region of about 40nucleotides in stem-loop II has been identified by Cook, et al. (NucleicAcids Research, 19:1577–1583). This binding region can be target forgeneration of RNA/DNA duplexes (e.g., Li et al., J. Virol.,67:6882–6888, 1993) using one or more thiophosphoramidateoligonucleotides, according to the methods of the present invention.

The HIV-1 TAT is essential for viral replication and is a potenttransactivator of long terminal repeat (LTR)-directed viral geneexpression (Dayton et al., Cell, 44:941–947, 1986; Fisher et al.,Nature, 320:367–371, 1986). Transactivation induced by TAT proteinrequires the presence of the TAR element (See U.S. Pat. No. 5,837,835)which is located in the untranslated 5′ end of the viral mRNA element.

The TAR element is capable of forming a stable stem-loop structure(Muesing et al., Cell, 48:691–701, 1987). The integrity of the stem anda 3 nucleotide (nt) bulge on the stem of TAR has been demonstrated to beessential for specific and high-affinity binding of the TAT protein tothe TAR element (Roy et al., Genes Dev., 4:1365–1373, 1990; Cordingleyet al., Proc. Natl. Acad. Sci., 87:8985–8989, 1990; Dingwall et al.,Proc. Natl. Acad. Sci., 86:6925–6929, 1989; Weeks et al., Science,249:1281–1285, 1990). This region can be targeted for anti-sense therapyfollowing the method of the present invention.

In addition to targeting the RNA binding sites of the REV, RRE and TATproteins, the RNA coding sequences for the REV and TAT proteinsthemselves can be targeted in order to block expression of the proteins.

Initial screening of N3′→P5′ thiophosphoramidate oligonucleotides,directed to bind potential antisense target sites, typically includestesting for the thermal stability of resultant RNA/DNA duplexes. When athiophosphoramidate oligonucleotide is identified that binds a selectedRNA target sequence, the oligonucleotide is further tested forinhibition of RNA function in vitro. Cell culture assays systems areused for such in vitro analysis (e.g., herpes simplex virus, Kulka etal., Antiviral Res., 20:115–130, 1993; HIV-1, Li et al., J. Virol.,67:6882–6888, 1993, Vickers et al., Nucleic Acids Research,19:3359–3368, 1991; coronary smooth muscle cell proliferation inrestenosis, Zalewski et al., Nucleic Acids Research, 15:1699–1715, 1987;IL-2R, Grigoriev et al., Proc. Natl. Acad. Sci., 90:3501–3505, 1993;c-myb, Baer et al., Blood, 79:1319–1326, 1992; c-fos, Cutry et al., J.Biol. Chem., 264:19700–19705, 1989; BCR/ABL, Szczylik et al., Science,253:562–565, 1991).

C. Anti-Gene Applications

Inhibition of gene expression via triplex formation has been previouslydemonstrated (Cooney et al., Science, 241:456–459, 1989; Orson et al.,Nucleic Acids Research, 19:3435–3441, 1991; Postel et al., Proc. Natl.Acad. Sci., 88:8227–8231, 1991). The increased stability of triplexstructures formed when employing third strand thiophosphoramidate analogoligonucleotides provides a stronger tool for antigene applications,including veterinary and human therapeutic applications.

A target region of choice is selected based on known sequences usingstandard rules for triplex formation (Helene and Toulme, Biochem.Biophys. Acta, 1049:99–125, 1990). Typically, the thiophosphoramidateoligonucleotide sequence is targeted against double-stranded geneticsequences in which one strand contains predominantly purines and theother strand contains predominantly pyrimidines.

Thiophosphoramidate oligonucleotides of the present invention are testedfor triplex formation against a selected duplex target sequences usingband shift assays (see for example, U.S. Pat. No. 5,726,297, Example 4).Typically, high percentage polyacrylamide gels are used for band-shiftanalysis and the levels of denaturing conditions (Ausubel et al.,Current Protocols in Molecular Biology, John Wiley and Sons, Inc. MediaPa.; Sauer et al. Editor, Methods in Enzymology Protein/DNAInteractions, Academic Press, 1991; Sambrook et al., In MolecularCloning: A Laboratory Manual, Cold Spring Harbor Press, Vol. 2, 1989)are adjusted to reduce any non-specific background binding.

The duplex target is labeled (for example, using a radioactivenucleotide) and mixed with a third strand oligonucleotide, being testedfor its ability to form triplex structures with the target duplex. Ashift of the mobility of the labeled duplex oligonucleotide indicatesthe ability of the oligonucleotide to form triplex structures.

Triplex formation is indicated in the band shift assay by a decreasedmobility in the gel of the labeled triplex structure relative to thelabeled duplex structure.

Numerous potential target sites can be evaluated by this methodincluding target sites selected from a full range of DNA sequences thatvary in length as well as complexity. Sequence-specificthiophosphoramidate analog binding molecules are potentially powerfultherapeutics for essentially any disease or condition that in some wayinvolves DNA. Exemplary target sequences for such therapeutics include:a) DNA sequences involved in the propagation and/or maintenance ofinfectious agents, such as, bacterial, viruses, yeast and other fungi,for example, disrupting the metabolism of an infectious agent; and b)sequences causing inappropriate expression or proliferation of cellulargenes, such as oncogenes, for example, blocking or reducing thetranscription of inappropriately expressed cellular genes (such as genesassociated with certain genetic disorders).

Gene expression or replication can be blocked by generating triplexstructures in regions to which required regulatory proteins (ormolecules) are known to bind (for example, HIV transcription associatedfactors like promoter initiation sites and SP1 binding sites, McShan etal., J. Biol. Chem., 267:5712–5721, 1992). Alternatively, specificsequences within protein-coding regions of genes (e.g., oncogenes) canbe targeted as well.

When a thiophosphoramidate analog oligonucleotide is identified thatbinds a selected duplex target sequence tests, for example, by the gelband shift mobility assay described above, the analog is further testedfor its ability to form stable triplex structures in vitro. Cell cultureand in vivo assay systems, such as those described U.S. Pat. No.5,631,135, are used.

Target sites can be chosen in the control region of the genes, e.g., inthe transcription initiation site or binding regions of regulatoryproteins (Helene and Toulme, 1990; Birg et al., 1990; Postel et al.,1991; Cooney et al., 1988). Also, target sites can be chosen such thatthe target also exists in mRNA sequences (i.e., a transcribed sequence),allowing oligonucleotides directed against the site to function asantisense mediators as well (see above).

Also, thiophosphoramidate modified DNA molecules can be used to generatetriplex molecules with a third strand target (i.e., a single-strandnucleic acid). For example, a DNA molecule having two regions capable offorming a triplex structure with a selected target third strand moleculecan be synthesized. Typically the two regions are linked by a flexibleregion which allows the association of the two regions with the thirdstrand to form a triplex.

Hinge regions can comprise any flexible linkage that keeps the twotriplex forming regions together and allows them to associate with thethird strand to form the triplex. Third strand targets are selected tohave appropriate purine/pyrimidine content so as to allow formation oftriplex molecules.

The flexible linkage may connect the two triplex forming regions(typically, complementary DNA strands) in any selected orientationdepending on the nature of the base sequence of the target. For example,the two triplex forming regions each have 5′ and 3′ ends, these ends canbe connected by the flexible hinge region in the following orientations:5′ to 3′, 3′ to 5′, 3′ to 3′, and 5′ to 5′.

Further, duplex DNA molecules containing at least onethiophosphoramidate linkage in each strand can be used as decoymolecules for transcription factors or DNA binding proteins (e.g.,c-myb).

Single-stranded DNA can also be used as a target nucleic acid foroligonucleotides of the present invention, using, for example,thiophosphoramidate intersubunit linkage-containing hairpin structures.Two thiophosphoramidate analog oligonucleotides can be selected forsingle-strand DNA target-directed binding. Binding of the twophosphoramidate analog strands to the single-strand DNA target resultsin formation of a triplex.

D. Pharmaceutical Compositions

The present invention includes pharmaceutical compositions useful inantisense and antigene therapies. The compositions comprise an effectiveamount of N3′→P5′ thiophosphoramidate oligonucleotides in combinationwith a pharmaceutically acceptable carrier. One or more N3′→P5′thiophosphoramidate oligonucleotides (having different base sequences orlinkages) may be included in any given formulation.

The N3′→P5′ thiophosphoramidate oligonucleotides, when employed intherapeutic applications, can be formulated neat or with the addition ofa pharmaceutical carrier. The pharmaceutical carrier may be solid orliquid. The formulation is then administered in a therapeuticallyeffective dose to a subject in need thereof.

Liquid carriers can be used in the preparation of solutions, emulsions,suspensions and pressurized compositions. The N3′→P5′thiophosphoramidate oligonucleotides are dissolved or suspended in apharmaceutically acceptable liquid excipient. Suitable examples ofliquid carriers for parenteral administration of N3′→P5′thiophosphoramidate oligonucleotides preparations include water(partially containing additives, e.g., cellulose derivatives, preferablysodium carboxymethyl cellulose solution), alcohols (including monohydricalcohols and polyhydric alcohols, e.g., glycols) and their derivatives,and oils (e.g., fractionated coconut oil and arachis oil). The liquidcarrier can contain other suitable pharmaceutical additives including,but not limited to, the following: solubilizers, suspending agents,emulsifiers, buffers, thickening agents, colors, viscosity regulators,preservatives, stabilizers and osmolarity regulators.

For parenteral administration of N3′→P5′ thiophosphoramidateoligonucleotides the carrier can also be an oily ester such as ethyloleate and isopropyl myristate. Sterile carriers are useful in sterileliquid form compositions for parenteral administration.

Sterile liquid pharmaceutical compositions, solutions or suspensions canbe utilized by, for example, intraperitoneal injection, subcutaneousinjection, intravenously, or topically. For example, antisenseoligonucleotides directed against retinal cytomegalovirus infection maybe administered topically by eyedrops. N3′→P5′ thiophosphoramidateoligonucleotides can also be administered intravascularly or via avascular stent impregnated with mycophenolic acid, for example, duringballoon catheterization to provide localized anti-restenosis effectsimmediately following injury.

The liquid carrier for pressurized compositions can be halogenatedhydrocarbon or other pharmaceutically acceptable propellant. Suchpressurized compositions may also be lipid encapsulated for delivery viainhalation. For administration by intranasal or intrabronchialinhalation or insufflation, N3′→P5′ thiophosphoramidate oligonucleotidesmay be formulated into an aqueous or partially aqueous solution, whichcan then be utilized in the form of an aerosol, for example, fortreatment of infections of the lungs like Pneumocystis carnii.

N3′→P5′ thiophosphoramidate oligonucleotides may be administeredtopically as a solution, cream, or lotion, by formulation withpharmaceutically acceptable vehicles containing the active compound. Forexample, for the treatment of genital warts.

The N3′→P5′ thiophosphoramidate oligonucleotides may be administered inliposome carriers. The use of liposomes to facilitate cellular uptake isdescribed, for example, in U.S. Pat. No. 4,897,355 and U.S. Pat. No.4,394,448. Numerous publications describe the formulation andpreparation of liposomes.

The dosage requirements for treatment with N3′→P5′ thiophosphoramidateoligonucleotides vary with the particular compositions employed, theroute of administration, the severity of the symptoms presented, theform of N3′→P5′ thiophosphoramidate oligonucleotides and the particularsubject being treated.

For use as an active ingredient in a pharmaceutical preparation, anoligonucleotide of this invention is generally purified away from otherreactive or potentially immunogenic components present in the mixture inwhich they are prepared. Typically, each active ingredient is providedin at least about 90% homogeneity, and more preferably 95% or 99%homogeneity, as determined by functional assay, chromatography, or gelelectrophoresis. The active ingredient is then compounded into amedicament in accordance with generally accepted procedures for thepreparation of pharmaceutical preparations.

Pharmaceutical compositions of the invention can be administered to asubject in a formulation and in an amount effective to achieve anyclinically desirable result. For the treatment of cancer, desirableresults include reduction in tumor mass (as determined by palpation orimaging; e.g., by radiography, CAT scan, or MRI), reduction in the rateof tumor growth, reduction in the rate of metastasis formation (asdetermined e.g., by histochemical analysis of biopsy specimens),reduction in biochemical markers (including general markers such as ESR,and tumor-specific markers such as serum PSA), and improvement inquality of life (as determined by clinical assessment, e.g., Karnofskyscore). For the treatment of viral infection, desirable results includereduction or elimination of the infection, the formation of infectiousparticles, or resolution of disease-associated symptoms.

The amount of oligonucleotide per dose and the number of doses requiredto achieve such effects can be determined empirically using in vitrotests and animal models (illustrated in Example 9). An appropriate rangefor testing can be estimated from the 50% inhibitory concentrationdetermined with isolated telomerase or cultured cells. Preparations ofisolated telomerase can be obtained according to U.S. Pat. No.5,968,506. Typically, the formulation and route of administration willprovide a local concentration at the disease site of between 1 μM and 1nM for a stable oligonucleotide of 12–15 nucleosides that is 100%identical to an enzyme-specific target RNA sequence. The ultimateresponsibility for determining the administration protocol is in thehands of the managing clinician.

In general, N3′→P5′ thiophosphoramidate oligonucleotides areadministered at a concentration that affords effective results withoutcausing any harmful or deleterious side effects (e.g., an effectiveamount). Such a concentration can be achieved by administration ofeither a single unit dose, or by the administration of the dose dividedinto convenient subunits at suitable intervals throughout the day.

E. Diagnostic Applications

The thiophosphoramidate oligonucleotides of the present invention arealso useful in diagnostic assays for detection of RNA or DNA having agiven target sequence. In one general application, thethiophosphoramidate oligonucleotides are labeled (e.g., isotopically orother detectable reporter group) and used as probes for DNA or RNAsamples that are bound to a solid support (e.g., nylon membranes).

Alternatively, the thiophosphoramidate oligonucleotides may be bound toa solid support (for example, magnetic beads) and homologous RNA or DNAmolecules in a sample separated from other components of the samplebased on their hybridization to the immobilized phosphoramidate analogs.Binding of thiophosphoramidate oligonucleotides to a solid support canbe carried out by conventional methods. Presence of the bound RNA or DNAcan be detected by standard methods, for example, using a second labeledreporter or polymerase chain reaction (See U.S. Pat. Nos. 4,683,195 and4,683,202).

Diagnostic assays can be carried out according to standard procedures,with suitable adjustment of the hybridization conditions to allowthiophosphoramidate oligonucleotide hybridization to the target region.The ability of thiophosphoramidate oligonucleotides to bind at elevatedtemperature can also help minimize competition for binding to a targetsequence between the thiophosphoramidate oligonucleotides probe and anycorresponding single-strand phosphodiester oligonucleotide that ispresent in the diagnostic sample.

Thiophosphoramidate oligonucleotides designed for use in hybridizationassays and other protocols described in this disclosure can be packagedin kit form. The oligonucleotide is provided in a container, typicallyin a buffer suitable for long-term storage, and is optionallyaccompanied by other reagents, standards, or controls useful inconducting the reaction. Typically, the kit will also be accompanied bywritten indications for use of the oligonucleotide in a hybridizationreaction or diagnostic assay, either as a product insert or byassociated literature in distribution or marketing of the kit.

F. Other Applications

In one aspect, the thiophosphoramidate oligonucleotides can be used inmethods to enhance isolation of RNA or DNA from samples. For example, asdiscussed above, thiophosphoramidate oligonucleotides can be fixed to asolid support and used to isolate complementary nucleic acid sequences,for example, purification of a specific mRNA from a polyA fraction(Goldberg et al., Methods in Enzmology, 68:206, 1979). Thethiophosphoramidate oligonucleotides are advantageous for suchapplications since they can form more stable interactions with RNA andduplex DNA than standard phosphodiester oligonucleotides.

A large number of applications in molecular biology can be found forreporter labeled thiophosphoramidate oligonucleotides, particularly forthe detection of RNA in samples. Thiophosphoramidate oligonucleotidescan be labeled with radioactive reporters (³H, ¹⁴C, ³²P, or ³⁵Snucleosides), biotin or fluorescent labels (Gryaznov et al., NucleicAcids Research, 20:3403–3409, 1992). Labeled thiophosphoramidateoligonucleotides can be used as efficient probes in, for example, RNAhybridization reactions (Ausubel et al., Current Protocols in MolecularBiology, John Wiley and Sons, Inc., Media, Pa.; Sambrook et al., InMolecular Cloning: A Laboratory Manual, Cold Spring Harbor LaboratoryPress, Vol. 2, 1989).

Also, double-stranded DNA molecules where each strand contains at leastone thiophosphoramidate linkage can be used for the isolation ofDNA-duplex binding proteins. In this embodiment the duplex containingthiophosphoramidate intersubunit linkages is typically affixed to asolid support and sample containing a suspected binding protein is thenpassed over the support under buffer conditions that facilitate thebinding of the protein to its DNA target. The protein is typicallyeluted from the column by changing buffer conditions.

The triplex forming DNA molecules described above, containingthiophosphoramidate modified linkages, can be used as diagnosticreagents as well, to, for example, detect the presence of a DNA moleculein a sample.

Further, complexes containing oligonucleotides having N3′→P5′thiophosphoramidate intersubunit linkages can be used to screen foruseful small molecules or binding proteins: for example, N3′→P5′thiophosphoramidate oligonucleotide complexes with duplex DNA can beused to screen for small molecules capable of further stabilizing thetriplex structure. Similar screens are useful with N3′→P5′thiophosphoramidate oligonucleotide complexes formed with single strandDNA and RNA molecules.

G. Variations

Variations on the thiophosphoramidate oligonucleotides used in themethods of the present invention include modifications to facilitateuptake of the oligonucleotide by the cell (e.g., the addition of acholesterol moiety (Letsinger, U.S. Pat. No. 4,958,013); production ofchimeric oligonucleotides using other intersubunit linkages (Goodchild,Bioconjugate Chem., 1:165–187, 1990); modification with intercalatingagents (for example, triplex stabilizing intercalating agents, Wilson etal., Biochemistry, 32:10614–10621, 1993); and use of ribose instead ofdeoxyribose subunits.

Further modifications include, 5′ and 3′ terminal modifications to theoligonucleotides (e.g., —OH, —OR, —NHR, —NH₂ and cholesterol). Inaddition, the ribose 2′ position can be the site of numerousmodifications, including, but not limited to, halogenation (e.g., —F).

N3′→P5′ thiophosphoramidate oligonucleotides may also be modified byconjugation to a polypeptide that is taken up by specific cells. Suchuseful polypeptides include peptide hormones, antigens and antibodies.For example, a polypeptide can be selected that is specifically taken upby a neoplastic cell, resulting in specific delivery of N3′→P5′thiophosphoramidate oligonucleotides to that cell type. The polypeptideand oligonucleotide can be coupled by means known in the art (see, forexample, PCT International Application Publication No. PCT/US89/02363,WO 89/12110, published Dec. 14, 1989, Ramachandr, K. et al.).

The properties of such modified thiophosphoramidate oligonucleotides,when applied to the methods of the present invention, can be determinedby the methods described herein.

EXAMPLE 1 General Methods

³¹P NMR spectra were obtained on a Varian 400 Mhz spectrometer. ³¹P NMRspectra were referenced against 85% aqueous phosphoric acid. Anionexchange HPLC was performed using a Dionex DX 500 Chromatography System,with a Pharmacia Bitotech Mono Q HR 5/5 or 10/16 ion exchange columns.Mass spectral analysis was performed by Mass Consortium, San Diego,Calif. MALDI-TOF analysis of oligonucleotides was obtained using aPerSpective Biosystems Voyager Elite mass spectrometer with delayedextraction. Thermal dissociation experiments were conducted on a CaryBio 100 UV-Vis spectrometer.

All reactions were carried out in oven dried glassware under a nitrogenatmosphere unless otherwise stated. Commercially available DNA synthesisreagents were purchased from Glen Research (Sterling, Va.). Anhydrouspyridine, toluene, dichloromethane, diisopropylethyl amine,triethylamine, acetic anhydride, 1,2-dichloroethane, and dioxane werepurchased from Aldrich (Milwaukee, Wis.).

All non-thiophosphoramidate oligonucleotides were synthesized on an ABI392 or 394 DNA synthesizer using standard protocols for thephosphoramidite based coupling approach (Caruthers, Acc. Chem. Res.,24:278–284, 1991). The chain assembly cycle for the synthesis ofoligonucleotide phosphoramidates was the following: (i) detritylation,3% trichloroaceticacid in dichloromethane, 1 min; (ii) coupling, 0.1 Mphosphoramidite and 0.45 M tetrazole in acetonitrile, 10 min; (iii)capping, 0.5 M isobutyic anhydride in THF/lutidine, 1/1, v/v, 15 sec;and (iv) oxidation, 0.1 M iodine in THF/pyridine/water, 10/10/1, v/v/v,30 sec.

Chemical steps within the cycle were followed by acetonitrile washingand flushing with dry argon for 0.2–0.4 min. Cleavage from the supportand removal of base and phosphoramidate protecting groups was achievedby treatment with ammonia/EtOH, 3/1, v/v, for 6 h at 55° C. Theoligonucleotides were concentrated to dryness in vacuo after which the2′-t-butyldimethylsilyl groups were removed by treatment with 1M TBAF inTHF for 4–16 h at 25° C. The reaction mixtures were diluted with waterand filtered through a 0.45 nylon acrodisc (from Gelman Sciences, AnnArbor, Mich.). Oligonucleotides were then analyzed and purified by IEHPLC and finally desalted using gel filtration on a Pharmacia NAP-5 orNAP-25 column. Gradient conditions for IE HPLC: solvent A (10 mM NaOH),solvent B (10 mM NaOH and 1.5 M NaCl); solvent A for 3 min then a lineargradient 0–80% solvent B within 50 min.

EXAMPLE 2 Synthesis of Arabino-fluorooligonucleotide N3′→P5′Phosphoramidates

The solid phase synthesis of oligo-2′-arabino-fluoronucleotide N3′→P5′phosphoramidates was based on the phosphoramidite transfer reactionemploying the monomer buildingblocks—5′-(O-cyanoethyl-N,N′-diisopropylamino)-phosphoramidites of3′-MMTr-protected-3′-amino-2′-ara-fluoro nucleosides. Preparation of thenucleoside monomers is depicted in Scheme 4.

Sugar precursor 1 (from Pfanstiehl) was converted into the α-1-bromointermediate 2 with retention of sugar C-1 configuration. Compound 2 wasthen used, without isolation, for a S_(N)2-type glycosylation reactionwith silylated uracil and thymine bases, which resulted in formation ofnucleosides 3. Stereo selectivity of the glycosylation reaction wasquite high—more than 90% of the formed nucleoside 3 had the desiredβ-anomeric configuration, as was judged by ¹H NMR analysis of thereaction mixture. The pure β-isomer of nucleoside 3 was isolated bycrystallization from ethanol. Subsequently, 5′- and 3′-O-benzoylprotecting groups of 3 were removed in near quantitative yields bytreatment with methanolic ammonia. The resultant 5′-,3′-hydroxyl groupscontaining nucleoside product was then converted into the2,3′-anhydronucleoside 4 under Mitsunobu reaction conditions. Thetreatment of the 2,3′-anhydronuclesides with lithium azide yielded thekey 3′-azido precursor 5. This compound was then converted intophosphoramidites 7t,u by the catalytic reduction of 3′-azido to 3′-aminogroup by hydrogenation, followed by 3′-tritylation, 5′-O-deprotectionand 5′-O-phosphitylation. Cytidine phosphoramidite 7c was obtained fromthe 3′-azido precursor using the uracil-to-cytosine conversion process.Total yields of the phosphoramidites 7c,t,u were in the range of 8–12%based on the starting sugar precursor 1. Structure of the monomers wasconfirmed by ¹H, ³¹P, ¹⁹F NMR and by mass spectrometric analysis.Oligonucleotide synthesis using the 2′-arabino-fluoronucleotide monomerwas then conducted on an automated DNA/RNA ABI 394 synthesizer asdescribed below.

EXAMPLE 3 Synthesis of Oligonucleotide N3′→P5′ Thiophosphoramidates

Oligonucleotide N3′→P5′ thiophosphoramidates were prepared by theamidite transfer reaction on an ABI 394 synthesizer. The fully protectedmonomer building blocks were 3′-aminotritylnucleoside-5′-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite wherenucleoside is 3′-deoxy-thymidine, 2′,3′-dideoxy-N²-isobutyryl-guanosine,2′,3′-dideoxy-N⁶-benzoyl-adenosine or 2′,3′-dideoxy-N⁴-benzoyl-cytidine.5′-Succinyl-3′-aminotrityl-2′,3′-dideoxy nucleosides were coupled withan amino group containing long chain controlled pore glass (LCAA-CPG)and used as the solid support. The synthesis was performed in thedirection of 5′ to 3′. The following protocol was used for the assemblyof oligonucleotide N3′→P5′ thiophosphoramidates: (i) detritylation, 3%dichloroacetic acid in dichloromethane; (ii) coupling, 0.1 Mphosphoramidite and 0.45 M tetrazole in acetonitrile, 25 sec; (iii)capping, isobutyric anhydride/2,6-lutidine/THF 1/1/8 v/v/v as Cap A andstandard Cap B solution; (iv) sulfurization, 15% S₈ in carbon disulfidecontaining 1% triethylamine, 1 min. Before and after the sulfurizationstep, the column was washed with neat carbon disulfide to preventelemental sulfur precipitation. The oligonucleotide thiophosphoramidateswere cleaved from the solid support and deprotected with concentratedaqueous ammonia. The compounds were analyzed and purified by HPLC. Ionexchange (IE) HPLC was performed using DIONEX DNAPac™ ion exchangecolumn at pH 12 (10 mM NaOH) with a 1%/min linear gradient of 10 mM NaOHin 1.5 M NaCl and a flow rate of 1 ml/min. The products were desalted onSephadex NAP-5 gel filtration columns (Pharmacia) and lyophilized invacuo. ³¹P NMR experiments were performed in deuterium oxide to analyzethe extent of sulfurization analysis (³¹P NMR δ, ppm 58, 60 broadsignals Rp,Sp isomers).

Oligonucleotide thiophosphoramidate 5′-GTTAGGGTTAG-3′ (SEQ ID NO:1) wassynthesized the following way: An ABI Model 394 synthesizer was set upwith 0.1M solutions of 3′-tritylamino-2′,3′-dideoxy-N-benzoyl-adenosine(N²-isobutyryl-guanosine, and thymidine)5′-(2-cyanoethyl-N,N-diisopropyl)phosphoramidites. The reagent bottle ofstation #10 was filled with neat carbon disulfide and reagent bottle #15was filled with a solution of 15% S₈ in carbon disulfide containing 1%triethylamine. As the activator the commercially available 0.45 Msolution of tetrazole in acetonitrile was used. Cap A solution (station#11) was replaced by tetrahydrofuran/isobutyric anhydride/2,6-lutidine8/1/1 v/v/v solution. Cap B was also the commercially available reagent.A new function was created to deliver carbon disulfide from station #10to the column. The default sulfur synthesis cycle was modified thefollowing way: sulfurization time was set at 1 min., and before andafter sulfurization carbon disulfide was delivered to the column for 20s. The synthesis column was filled with 1 μmole solid supportN²-isobutyryl-3′-(trityl)amino-2′,3′-dideoxyguanosine-5′-succinyl-loadedCPG (controlled pore glass). The sequence of the compound was programmedas GATTGGGATTG (5′→3′) (SEQ ID NO:9). The trityl group was removed atend of the synthesis and the column was washed manually with carbondisulfide and acetonitrile. The solid support was removed from thecolumn and treated with 1 ml concentrated aqueous ammonia at 55° C. for6 hr in a tightly closed glass vial. After filtration most of theammonia was evaporated and the remaining solution was desalted usingSephadex™ NAP-5 gel filtration columns (Pharmacia) followed bylyophilization in vacuo. The product was analyzed and purified asdescribed above. All of the other thiophosphoramidate oligonucleotideslisted in Table 2 (SEQ ID NOs:2–4) were synthesized using the abovedescribed methods.

EXAMPLE 4 Acid Stability and Duplex Formation Properties ofOligonucleotide N3′→P5′ Thiophosphoramidates

Oligonucleotide thiophosphoramidates unexpectedly demonstrated anincreased acid stability relative to phosphoramidate counterparts. Onemight have expected that substitution of the non-bridge oxygen of theinternucleotide phosphate group with sulfur should have resulted in adecrease in the acid stability of the phosphoramidate because thedifference in the electron-donating properties of sulfur verses oxygen,which could have made the protonation of the 3′-NH easier. However,contrary to this prediction, the thiophosphoramidate internucleotidelinkages were found to be more acid stable than theiroxo-phosphoramidate counterparts.

The half-lives of thiophosphoramidate TAG₃T₂AGACA₂ (SEQ ID NO:2) and itsphosphoramidate counterpart in 40% aqueous acetic acid at roomtemperature were approximately 6 hours and 0.5 hour, respectively,according to IE HPLC analysis (see Table 1). Moreover, the compositionof the hydrolysis products was different between the thiophosphoramidateand its phosphoramidate counterpart. The acid hydrolysis of thethiophosphoramidate appears to initially result in de-sulfurization,rather than cleavage of internucleoside N—P groups, as it occurs for thephosphoramidates. These results indicated a much higher resistance toacidic conditions of the thiophosphoramidates than that of thephosphoramidate oligonucleotides, thus indicating that this new class ofthiophosphoramidate oligonucleotides has improved potential for thedevelopment of oral oligonucleotide therapeutics as compared to otherphosphoramidate oligonucleotides.

TABLE 1 Tm, −Tm, Acid Expt Oligomer Type^(a) ° C.^(b) ° C.^(c)Stability^(d) 1. GTTAGGGTTAG po 44.2 — SEQ ID NO:1 2. TAGGGTTAGACAA po45.2 — SEQ ID NO:2 3. Same as expt 1 np 72.1 27.9 4. Same as expt 2 np71.7 26.5 0.5 hr 5. Same as expt 1 nps 71.5 27.3 6. Same as expt 2 nps70.0 24.8   6 hr ^(a)po, np, nps correspond to phosphodiester,N3′→P5′ phosphoramidate and thiophosphoramidate groups, respectively;

Duplex formation properties of oligonucleotide phosphoramidates withcomplementary RNA strand were evaluated using thermal dissociationexperiments. The results are summarized in Table 1. The presented datashow that the oligonucleotide thiophosphoramidates formed significantlymore stable complexes than the isosequential natural phosphodiesteroligomers wherein the difference in Tm was ˜25–27° C. per oligomer.Also, the increase in the thermal stability of duplexes was similar tothat observed for the phosphoramidate oligomers. This indicates that thesubstitution of non-bridging oxygen by sulfur atom in internucleosidephosphoramidate group did not alter RNA binding properties of thesecompounds significantly, which was determined by N-type sugar puckeringof the 3′-aminonucleosides and by increased sugar-phosphate backbonehydration.

EXAMPLE 5 Preparation of Affinity Purified Extract Having TelomeraseActivity

Extracts used for screening telomerase inhibitors were routinelyprepared from 293 cells over-expressing the protein catalytic subunit oftelomerase (hTERT). These cells were found to have 2–5 fold moretelomerase activity than parental 293 cells. 200 ml of packed cells(harvested from about 100 liters of culture) were resuspended in anequal volume of hypotonic buffer (10 mM Hepes pH 7.9, 1 mM MgCl₂, 1 mMDTT, 20 mM KCl, 1 mM PMSF) and lysed using a dounce homogenizer. Theglycerol concentration was adjusted to 10% and NaCl was slowly added togive a final concentration of 0.3 M. The lysed cells were stirred for 30min and then pelleted at 100,000×g for 1 hr. Solid ammonium sulfate wasadded to the S100 supernatant to reach 42% saturation. The material wascentrifuged; the pellet was resuspended in one fifth of the originalvolume and dialyzed against Buffer ‘A’ containing 50 mM NaCl. Afterdialysis the extract was centrifuged for 30 min at 25,000×g. Prior toaffinity chromatography, Triton X-100™ (0.5 %), KCl (0.3 M) and tRNA (50μg/ml) were added. Affinity oligo (5′ biotinTEG-biotinTEG-biotinTEG-GTAGAC CTG TTA CCA guu agg guu ag 3′ [SEQ ID NO:5]; lower case represents2′O-methyl ribonucleotides and upper case represents deoxynucleotides)was added to the extract (1 nmol per 10 ml of extract). After anincubation of 10 min at 30° C., Neutravidin beads (Pierce; 250 μl of a50% suspension) were added and the mixture was rotated overnight at 4°C. The beads were pelleted and washed three times with Buffer ‘B’containing 0.3 M KCl, twice with Buffer ‘B’ containing 0.6 M KCl, andtwice more with Buffer B containing 0.3 M KCl. Telomerase was eluted inBuffer ‘B’ containing 0.3 M KCl, 0.15% Triton X-100™ and a 2.5 molarexcess of displacement oligo (5′-CTA ACC CTA ACT GGT AAC AGG TCT AC-3′[SEQ ID NO:6] at 0.5 ml per 125 μl of packed Neutravidin beads) for 30min. at room temperature. A second elution was performed and pooled withthe first. Purified extracts typically had specific activities of 10fmol nucleotides incorporated/min/μl extract, or 200 nucleotides/min/mgtotal protein.

Buffer ‘A’ Buffer ‘B’ 20 mM Hepes pH 7.9 20 mM Hepes pH 7.9  1 mM MgCl2 1 mM EDTA  1 mM DTT  1 mM DTT  1 mM EGTA 10% glycerol 10% glycerol 0.5Triton X-100 ™

EXAMPLE 6 Telomerase Inhibition by Oligonucleotide N3′→P5′Thiophosphoramidates

Three separate 100 μl telomerase assays are set up with the followingbuffer solutions: 50 mM Tris acetate, pH 8.2, 1 mM DTT, 1 mM EGTA, 1 mMMgCl₂, 100 mM K acetate, 500 μM dATP, 500 μM TTP, 10 μM [³²P-]dGTP (25Ci/mmol), and 100 nM d(TTAGGG)₃ [SEQ ID NO:7]. To the individualreactions 2.5, 5 or 10 μl of affinity-purified telomerase (see Example4) is added and the reactions are incubated at 37° C. At 45 and 90minutes, 40 μl aliquots are removed from each reaction and added to 160μl of Stop Buffer (100 mM NaCl, 10 mM Na pyrophosphate, 0.2% SDS, 2 mMEDTA, 100 μg/ml tRNA). 10 μl trichloroacetic acid (TCA) (100%) is addedand the sample is incubated on ice for 30 minutes. The sample ispelleted in a microcentrifuge (12000×g force) for 15 minutes. The pelletis washed with 1 ml 95% ethanol and pelleted again in themicrocentrifuge (12000×g force) for 5 minutes. The pellet is resuspendedin 50 μl dH₂O and transferred to a 12×75 glass test tube containing 2.5ml of ice cold solution of 5% TCA and 10 mM Na pyrophosphate. The sampleis incubated on ice for 30 minutes. The sample is filtered through a 2.5cm wet (dH₂O) GFC membrane (S&S) on a vacuum filtration manifold. Thefilter is washed three times under vacuum with 5 ml ice cold 1% TCA, andonce with 5 ml 95% ethanol. The filter is dried and counted in ascintillation counter using scintillation fluid. The fmol of nucleotideincorporated is determined from the specific activity of radioactivetracer. The activity of extract is calculated based on the dNTPincorporated and is expressed as fmol dNTP/min/μl extract.

Telomerase Activity Assay

Bio-Tel FlashPlate Assay

An assay is provided for the detection and/or measurement of telomeraseactivity by measuring the addition of TTAGGG telomeric repeats to abiotinylated telomerase substrate primer; a reaction catalyzed bytelomerase. The biotinylated products are captured instreptavidin-coated microtiter plates. An oligonucleotide probecomplementary to 3.5 telomere repeats labeled with ³³P is used formeasuring telomerase products, as described below. Unbound probe isremoved by washing and the amount of probe annealing to the capturedtelomerase products is determined by scintillation counting.

Method:

-   20. Thiophosphoramidate oligonucleotides were stored as concentrated    stocks and dissolved in PBS.-   21. For testing, the thiophosphoramidate oligonucleotides were    diluted to a 15× working stock in PBS and 2 μl was dispensed into    two wells of a 96-well microtiter dish (assayed in duplicate).-   22. Telomerase extract was diluted to a specific activity of    0.04–0.09 fmol DNTP incorporated/min./μl in Telomerase Dilution    Buffer and 18 μl added to each sample well to preincubate with    compound for 30 minutes at room temperature.-   23. The telomerase reaction was initiated by addition of 10 82 l    Master Mix to the wells containing telomerase extract and    oligonucleotide compound being tested. The plates were sealed and    incubated at 37° C. for 90 min.-   24. The reaction was stopped by the addition of 10 μl HCS.-   25. 25 μl of the reaction mixture was transferred to a 96-well    streptavidin-coated FlashPlate™ (NEN) and incubated for 2 hours at    room temperature with mild agitation.-   26. The wells were washed three times with 180 μl 2×SSC without any    incubation.-   27. The amount of probe annealed to biotinylated telomerase products    were detected in a scintillation counter.    Buffers:    Telomerase Dilution Buffer

50 mM Tris-acetate, pH 8.2

1 mM DTT

1 mM EGTA

1 mM MgCl₂

830 nM BSA

Master Mix (MM)

50 mM Tris-acetate, pH 8.2

1 mM DTT

1 mM EGTA

1 mM MgCl₂

150 mM K acetate

10 μM dATP

20 μM dGTP

120 μM dTTP

100 nM biotinylated primer (5′-biotin-AATCCGTCGAGCAGAGTT-3′) [SEQ IDNO:8]

5.4 nM labeled probe [5′-CCCTAACCCTAACCCTAACCC-(³³P) A₁₋₅₀-3′] [SEQ IDNO:9]; specific activity approximately 10⁹ cpm/μg or higher

Hybridization Capture Solution (HCS)

12×SSC (1×=150 mM NaCl/30 mM Na₃Citrate)

40 mM EDTA

40 mM Tris-HCl, pH 7.0

Using the foregoing assay, the thiophosphoramidate oligonucleotidesrepresented by SEQ ID NO:1 and SEQ ID NO:2 were shown to have telomeraseIC₅₀ values below 1.0 nM (see TABLE 2, Experiments 1 and 3).

TABLE 2 EVALUATION OF OLIGOS 1–4 AS TELOMERASE INHIBITORS IN COMPARISONWITH PHOSPHORAMIDATES: IC₅₀(nM) IC₅₀(nM) phos- thiophos- EXPOligonucleotide phoramidate phoramidate 20. 5′-GTTAGGGTTAG-3′ 1.9 0.89SEQ ID NO:1 21. 5′-GTTGAGTGTAG-3′ 1000 177.4 SEQ ID NO:3 22.5′-TAGGGTTAGACAA-3′ 1.64 0.41 SEQ ID NO:2 23. 5′-TAGGTGTAAGCAA-3′ 100079.3 SEQ ID NO:4

Oligonucleotide sequence 2 (SEQ ID NO:3) is a mismatch control for theoligonucleotides used in experiment 1 (SEQ ID NO:1). Similarly,oligonucleotide sequence 4 (SEQ ID NO:4) is a mismatch control for theoligonucleotides (SEQ ID NO:2) used in Experiment 3.

The telomerase inhibition data presented in Table 2 show that thethiophosphoramidate polynucleotides of the present invention are about2–3 times better at inhibiting telomerase activity relative tocounterpart phosphoramidates oligonucleotides. Thus, the inventivethiophosphoramidate oligonucleotides are not only more active in thetelomerase inhibition assay, as compared to their phosphoramidatecounterparts, but are also more acid resistant than them as well. Thiscombination of characteristics imparts the inventive thiophosphoramidateoligonucleotides with an important advantage compared to phosphoramidatepolynucleotides.

EXAMPLE 7 Anti-Tumor Activity of Thiophosphoramidate Oligonucleotides

Ex Vivo Studies

a. Reduction of Telomere Length in Tumor Cells

Colonies of human breast epithelial cells (spontaneously immortalized)were prepared using standard methods and materials. Colonies wereprepared by seeding 15-centimeter dishes with about 10⁶ cells in eachdish. The dishes were incubated to allow the cell colonies to grow toabout 80% confluence, at which time each of the colonies were dividedinto two groups. One group was exposed to a subacute dose ofthiophosphoramidate polynucleotide SEQ ID NO:2 at a predeterminedconcentration (e.g., between about 100 nM and about 20 μM) for a periodof about 4–8 hours after plating following the split. The second groupof cells were similarly exposed to mismatch control oligonucleotide SEQID NO:4.

Each group of cells is then allowed to continue to divide, and thegroups are split evenly again (near confluence). The same number ofcells were seeded for continued growth. The test thiophosphoramidateoligonucleotide or control oligonucleotide was added every fourth day tothe samples at the same concentration delivered initially. In oneexperiment the cells were additionally treated with FuGENE6™(Boehringer-Mannhiem) following manufacturers instructions. FuGENE6™enhances oligonucleotide uptake by the cells.

Telomere length was determined by digesting the DNA of the cell samplesusing restriction enzymes specific for sequences other than therepetitive T₂AG₃ sequence of human telomeres (TRF analysis). Thedigested DNA was separated by size using standard techniques of gelelectrophoresis to determine the lengths of the telomeric repeats, whichappear, after probing with a telomere DNA probe, on the gel as a smearof high-molecular weight DNA (approximately 2 Kb–15 Kb). FIGS. 4 and 5show examples of such experiments.

The results presented in FIG. 4 indicate that the thiophosphoramidateoligonucleotide SEQ ID NO:2 is a potent in vitro inhibitor of telomeraseactivity. In the absence of FuGENE6™, the thiophosphoramidateoligonucleotide SEQ ID NO:2 induced a large decrease in telomere lengthwhen incubated with HME50-5E cells in the range of 1–20 μM. When cellswere coincubated with FuGENE6 and thiophosphoramidate oligonucleotideSEQ ID NO:2 telomere size was reduced compared to the control cells ateven the lowest concentration tested (100 nM).

The results presented in FIG. 5 indicate that the thiophosphoramidateoligonucleotide having the sequence CAGTTAGGGTTAG (SEQ ID NO:8) is apotent in vitro inhibitor of telomerase activity. When the cells wereincubated with the thiophosphoramidate oligonucleotide SEQ ID NO:8,telomere size was reduced compared to the control cells at even thelowest concentration tested (1 nM). Thus, the inventivethiophosphoramidate oligonucleotides are potent in vitro inhibitors oftelomerase activity in immortalized human breast epithelial cell.

In another experiment, HME50-5E cells were incubated with one of thethiophosphoramidate polynucleotides shown in SEQ ID NOs:2 and 8. Themismatch oligonucleotide SEQ ID NO:4 was used as a control. Allpolynucleotides were used at concentrations between about 0.1 μM andabout 20 μM using the protocol described above. The data on cell growth,shown in FIG. 6, indicates that the cell entered crisis (i.e., thecessation of cell function) within about 100 days followingadministration of the test thiophosphoramidate oligonucleotides of theinvention.

In addition, TRF analysis of the cells (FIG. 7) using standardmethodology shows that the test thiophosphoramidate oligonucleotides ofthe invention were effective in reducing telomere length. The HME50-5Ecells were incubated with one of the thiophosphoramidate polynucleotidesshown in SEQ ID NOs:2 and 8. The mismatch oligonucleotide SEQ ID NO:4was used as a control. All polynucleotides were used at a concentrationof about 0.5 μM using the protocol described above. The length of thetelomeres were measured at 10, 20, 40 and 80 days. For the cells withthe control mismatch oligonucleotide, the telomere length was measuredat day 90, and this data point served as the end point. In addition tothe HME50-5E cells described above, this assay can be performed with anytelomerase-positive cell line, such as HeLa cells or HEK-293 cells.

b. Specificity

Thiophosphoramidate polynucleotides of the invention are screened foractivity (IC₅₀) against telomerase and other enzymes known to have RNAcomponents by performing hybridization tests or enzyme inhibition assaysusing standard techniques. Oligonucleotides having lower IC₅₀ values fortelomerase as compared to the IC₅₀ values toward the other enzymes beingscreened are said to possess specificity for telomerase.

c. Cytotoxicity

The cell death (XTT) assay for cytotoxicity was performed usingHME50-5E, Caki-1, A431, ACHN, and A549 cell types. The cell lines usedin the assay were exposed to the thiophosphoramidate oligonucleotide ofSEQ ID NO:2 for 72 hours at concentrations ranging from about 1 μM toabout 100 μM in the presence and absence of lipids. During this period,the optical density (OD) of the samples was determined for light at 540nanometers (nm). The IC₅₀ values obtained for the various cell types(shown in FIG. 8) were generally less than 1 μM. Thus, no significantcytotoxic effects are expected to be observed at concentrations lessthan about 100 μM. It will be appreciated that other tumor cells linessuch as the ovarian tumor cell lines OVCAR-5 and SK-OV-3 can be used todetermine cytotoxicity in addition to control cell lines such as normalhuman BJ cells. Other assays for cytotoxicity such as the MTT assay (seeBerridge et al., Biochemica, 4:14–19, 1996) and the alamarBlue™ assay(U.S. Pat. No. 5,501,959) can be used as well.

Preferably, to observe any telomerase inhibiting effects thethiophosphoramidate oligonucleotides should be administered at aconcentration below the level of cytotoxicity. Nevertheless, since theeffectiveness of many cancer chemotherapeutics derives from theircytotoxic effects, it is within the scope of the present invention thatthe thiophosphoramidate oligonucleotides of the present invention beadministered at any dose for which chemotherapeutic effects areobserved.

In Vivo Animal Studies

A human tumor xenograft model in which OVCAR-5 tumor cells are graftedinto nude mice can be constructed using standard techniques andmaterials. The mice are divided into two groups. One group is treatedintraperitoneally with a thiophosphoramidate oligonucleotides of theinvention. The other group is treated with a control comprising amixture of phosphate buffer solution (PBS) and an oligonucleotidecomplementary with telomerase RNA but has at least a one base mismatchwith the sequence of telomerase RNA. The average tumor mass for mice ineach group is determined periodically following the xenograft usingstandard methods and materials.

In the group treated with a thiophosphoramidate oligonucleotide of theinvention, the average tumor mass is expected to increase following theinitial treatment for a period of time, after which time the tumor massis expected to stabilize and then begin to decline. Tumor masses in thecontrol group are expected to increase throughout the study. Thus, thethiophosphoramidate oligonucleotides of the invention are expected tolessen dramatically the rate of tumor growth and ultimately inducereduction in tumor size and elimination of the tumor.

Thus, the present invention provides novel thiophosphoramidateoligonucleotides and methods for inhibiting telomerase activity andtreating disease states in which telomerase activity has deleteriouseffects, especially cancer. The thiophosphoramidate oligonucleotides ofthe invention provide a highly selective and effective treatment formalignant cells that require telomerase activity to remain immortal;yet, without affecting non-malignant cells.

All printed patents and publications referred to in this application arehereby incorporated herein in their entirety by this reference.

While the preferred embodiment of the invention has been illustrated anddescribed, it will be appreciated that various changes can be madetherein without departing from the spirit and scope of the invention.

1. A method of inhibiting human telomerase enzyme activity in a subjectin need thereof, comprising contacting the enzyme with anoligonucleotide comprising nucleoside subunits joined by inter-subunitlinkages, wherein the oligonucleotide comprises a contiguous sequence ofat least 10 nucleoside subunits complementary to the RNA component ofhuman telomerase, and wherein said at least 10 subunits are joined byN3′→N5′ thiophosphoramidate linkages having the structure3′-[—NH—P(═O)(SR)—O—]-5′, wherein R is selected from the groupconsisting of hydrogen, alkyl, and aryl; and pharmaceutically acceptablesalts thereof.
 2. A method of inhibiting proliferation of a cell thatexpresses human telomerase in vitro comprising contacting the cell withan oligonucleotide comprising nucleoside subunits joined byinter-subunit linkages, wherein the oligonucleotide comprises acontiguous sequence of at least 10 nucleoside subunits complementary tothe RNA component of human telomerase, and wherein said at least 10nucleoside subunits are joined by N3′→P5′ thiophosphoramidate linkageshaving the structure 3′-[—NH—P(═O))(—SR)—O—]-5′, wherein R is selectedfrom the group consisting of hydrogen, alkyl, and aryl; andpharmaceutically acceptable salts thereof.
 3. A method of inhibitingproliferation of a cancer cell that expresses human telomerase in asubject in need thereof comprising contacting the cell with anoligonucleotide comprising nucleoside subunits joined by inter-subunitlinkages, wherein the oligonucleotide comprises a contiguous sequence ofat least 10 nucleoside subunits complementary to the RNA component ofhuman telomerase, and wherein said at least 10 nucleoside subunits arejoined by N3n′→P5′ thiophosphoramidate linkage having the structure3′-[—NH—P(═O)(SR)—O—]-5′, wherein R is selected from the groupconsisting of hydrogen, alkyl, and pharmaceutically acceptable saltthereof.
 4. The method of claim 3 wherein the cell is a cell.
 5. Amethod of inhibiting human telomerase enzyme activity in vitro,comprising contacting the enzyme with an oligonucleotide comprisingnucleoside subunits joined by inter-subunit linkages, wherein theoligonucleotide comprises a contiguous sequence of at least 10nucleoside subunits complementary to the RNA component of humantelomerase, and wherein said at least 10 subunits are joined byN3′->N5′thiophosphoramidate linkages having the structure3′-[—NH—P(═O)(SR)—O—]-5′, wherein R is selected from the groupconsisting of hydrogen, alkyl, and aryl; and pharmaceutically acceptablesalts thereof.